\documentclass[12pt]{article}

% --------------
% setup packages
% --------------
\usepackage[english]{babel} % set default language to English
\usepackage[margin=.8in,top=1.1in,bottom=1.1in]{geometry} % page layout
\usepackage{amsmath,amsthm,amssymb,amsfonts} % math things
\usepackage{graphicx} % include graphics
\usepackage{titlesec} % help with section naming
\usepackage{xcolor} % color text [+ in math mode]
\usepackage{caption}
\usepackage{subcaption}
\usepackage{bookmark}
\usepackage{epsfig}
\usepackage[nottoc,numbib]{tocbibind} % add references to ToC
\usepackage{pifont} % for xmark == ding{53}
\usepackage{empheq} % for colorbox
\usepackage{mdframed} % for box around figures

\hypersetup{bookmarksopen=false,bookmarksnumbered=true}
\hypersetup{colorlinks=true,urlbordercolor=magenta}

% -------------
% custom colors
% -------------
\definecolor{darkgray}{RGB}{100, 100, 100}
\definecolor{darkergray}{RGB}{66, 66, 66}
\definecolor{gray}{rgb}{0.5,0.5,0.5}
\definecolor{orange}{rgb}{1.0,0.3,0.01}
\definecolor{violet}{rgb}{0.4,0.0,0.6}
\definecolor{yellow}{rgb}{1.0,0.7,0.0}
\definecolor{boxc}{rgb}{1.0, 1.0, .9}
\definecolor{mygreen}{rgb}{0, 0.75, 0.18}

% ----------------
% custom shortcuts
% ----------------
\renewcommand{\l}{\left}
\renewcommand{\r}{\right}
\renewcommand{\b}[1]{\textbf{\textit{#1}}}
\renewcommand{\t}[1]{\widehat{#1}}
\renewcommand{\u}[1]{\underline{#1}}
\newcommand{\bs}[1]{\boldsymbol{#1}}
\newcommand{\mb}[1]{\mathbf{#1}}
\newcommand{\mc}[1]{\mathcal{#1}}
\newcommand{\tb}[1]{\textbf{#1}}
\def\bg#1\eg{%
    \begin{gather}%
    #1%
    \end{gather}%
}

% --------------
% custom symbols
% --------------
\newcommand{\E}{\mathbb{E}}
\newcommand{\D}{\mathbb{D}}
\newcommand{\N}{\mathbb{N}}
\newcommand{\R}{\mathbb{R}}
\renewcommand{\P}{\mathbb{P}}

% ---------------
% custom commands
% ---------------
\newcommand{\boldmm}[1]{\textbf{\textit{#1}}}
\newcommand{\comment}[1]{ \color{darkgray}\left[\text{#1}\right]\color{black}}
\newcommand{\commenttwo}[2]{\color{darkgray}\left[\begin{array}{c}\text{#1}\\ \text{#2}\end{array}\right]\color{black}}
\newcommand{\gooditem}{\item[\checkmark]}
\newcommand{\baditem}{\item[\ding{53}]}
\newcommand{\evalat}[1]{\biggr\rvert _{#1}}
\newcommand{\bad}{\textbf{\color{red}[\ding{53}]} }
\newcommand{\good}{\textbf{\color{green}[\checkmark]} }

% ---------
% color box
% ---------
\newlength\mytemplen
\newsavebox\mytempbox

\makeatletter
\newcommand\mybox{%
    \@ifnextchar[%]
       {\@mybox}%
       {\@mybox[0pt]}}

\def\@mybox[#1]{%
    \@ifnextchar[%]
       {\@@mybox[#1]}%
       {\@@mybox[#1][0pt]}}

\def\@@mybox[#1][#2]#3{
    \sbox\mytempbox{#3}%
    \mytemplen\ht\mytempbox
    \advance\mytemplen #1\relax
    \ht\mytempbox\mytemplen
    \mytemplen\dp\mytempbox
    \advance\mytemplen #2\relax
    \dp\mytempbox\mytemplen
    \colorbox{boxc}{\hspace{0em}\usebox{\mytempbox}\hspace{0em}}}

\makeatother

% --------------
% begin document
% --------------
\begin{document}
	\pagenumbering{arabic}
	\begin{titlepage}
		\vspace*{0.1\paperheight}
		\centering
		\vspace*{8em}
		{\Huge \textbf{Boltzmann Machines}}\\
		\vspace*{1em}
		{\Large Yelysei Bondarenko}
		\vspace{0.2\paperheight}
	\end{titlepage}

	\pdfbookmark{Contents}{contents}
	\tableofcontents
	\setcounter{page}{1}
	
	\include{chapter_1}
	\include{chapter_2}
	\include{chapter_3}
	\include{chapter_4}
	\include{conclusions}

	\newpage
	\pdfbookmark{References}{references}
	
	\nocite{*}
	\bibliographystyle{ieee}
	\bibliography{bib}

\end{document}